Publications by authors named "Stephen Trudeau"

Article Synopsis
  • The updated PrePPI webserver predicts protein-protein interactions (PPIs) on a large scale for the human proteome using a Bayesian framework that combines structural and non-structural evidence.
  • It utilizes AlphaFold structures and template-based modeling to evaluate potential protein complexes, enabling comprehensive interaction predictions.
  • With a database containing about 1.3 million human PPIs, the webserver offers various features for exploring query proteins, visualizing 3D models, and accessing related information.
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Background: We tested whether proton pump inhibitors (PPIs) are associated with enteric infections among those with inflammatory bowel disease (IBD), after adequately accounting for baseline differences between PPI users and nonusers.

Methods: This was a self-controlled case series, with each patient serving as their own control. Ambulatory patients with IBD were included if they were tested for enteric infection by multiplex polymerase chain reaction testing panel (GIPCR) and/or Clostridoides difficile toxin PCR from 2015 to 2019 and received PPIs for some but not all of this period.

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Article Synopsis
  • - The updated PrePPI webserver predicts protein-protein interactions (PPIs) across the entire human proteome, utilizing a combination of structural and non-structural information through a Bayesian framework.
  • - It incorporates advanced structural modeling techniques, including AlphaFold for domain analysis, and provides a comprehensive database of approximately 1.3 million human PPIs that users can query.
  • - The server excels in performance, validated by its accuracy against established PPI databases, and offers tools for visualizing query proteins, creating 3D models, and exploring related features.
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We describe the Predicting Protein-Compound Interactions (PrePCI) database which comprises over 5 billion predicted interactions between 6.8 million chemical compounds and 19,797 human proteins. PrePCI relies on a proteome-wide database of structural models based on both traditional modeling techniques and the AlphaFold Protein Structure Database.

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Objectives: To evaluate clinical characteristics and outcomes of patients diagnosed with anterior (ASB) or lateral skull base (LSB) spontaneous cerebrospinal fluid (sCSF) leak.

Methods: Single center retrospective review of patients diagnosed with sCSF leaks of ASB or LSB between 1/1/2009 and 11/1/2019 (n = 69). Body mass index (BMI), gender, age at diagnosis, origin of CSF leak (ASB vs LSB), surgical approach, lumbar drain use, recurrence, pre-operative diagnosis of diabetes mellitus (DM), and obstructive sleep apnea (OSA) were collected.

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Epstein-Barr virus (EBV) causes endemic Burkitt lymphoma, the leading childhood cancer in sub-Saharan Africa. Burkitt cells retain aspects of germinal center B-cell physiology with MYC-driven B-cell hyperproliferation; however, little is presently known about their iron metabolism. CRISPR/Cas9 analysis highlighted the little-studied ferrireductase CYB561A3 as critical for Burkitt proliferation but not for that of the closely related EBV-transformed lymphoblastoid cells or nearly all other Cancer Dependency Map cell lines.

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Introduction & Objective: Children with cognitive delay often experience challenges with obtaining hearing thresholds through behavioral audiometry (BA). This necessitates sedated Auditory Brainstem Response (sABR) testing. This study aimed to evaluate diagnostic and hearing patterns in children with Down Syndrome (DS), Autism Spectrum Disorder (ASD), Global Developmental delay (GDD), and Cerebral Palsy (CP) who were unable to complete reliable BA testing due to severe cognitive delay.

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Epstein-Barr virus (EBV) infects 95% of adults worldwide and causes infectious mononucleosis. EBV is associated with endemic Burkitt lymphoma, Hodgkin lymphoma, posttransplant lymphomas, nasopharyngeal and gastric carcinomas. In these cancers and in most infected B-cells, EBV maintains a state of latency, where nearly 80 lytic cycle antigens are epigenetically suppressed.

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During the coronavirus 2019 pandemic, there has been a surge in production of remote learning materials for continued otolaryngology resident education. Medical students traditionally rely on elective and away subinternship experiences for exposure to the specialty. Delays and cancellation of clinical rotations have forced medical students to pursue opportunities outside of the traditional learning paradigm.

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Epstein-Barr virus (EBV) is associated with multiple human malignancies. To evade immune detection, EBV switches between latent and lytic programs. How viral latency is maintained in tumors or in memory B cells, the reservoir for lifelong EBV infection, remains incompletely understood.

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Epstein-Barr virus (EBV) causes infectious mononucleosis and is associated with multiple human malignancies. EBV drives B-cell proliferation, which contributes to the pathogenesis of multiple lymphomas. Yet, knowledge of how EBV subverts host biosynthetic pathways to transform resting lymphocytes into activated lymphoblasts remains incomplete.

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CD40 has major roles in B cell development, activation, and germinal center responses. CD40 hypoactivity causes immunodeficiency whereas its overexpression causes autoimmunity and lymphomagenesis. To systematically identify B cell autonomous CD40 regulators, we use CRISPR/Cas9 genome-scale screens in Daudi B cells stimulated by multimeric CD40 ligand.

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Epstein-Barr virus (EBV) causes Burkitt, Hodgkin, and post-transplant B cell lymphomas. How EBV remodels metabolic pathways to support rapid B cell outgrowth remains largely unknown. To gain insights, primary human B cells were profiled by tandem-mass-tag-based proteomics at rest and at nine time points after infection; >8,000 host and 29 viral proteins were quantified, revealing mitochondrial remodeling and induction of one-carbon (1C) metabolism.

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Purpose Of Review: Surgical mission trips in head and neck surgery are common. There are an increasing number of surgical groups performing complex reconstructions in low and middle-income countries (LMIC). Consideration of reconstructive options that are location and patient specific are critical for optimum patient care and local physician education.

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Epstein-Barr virus nuclear antigen (EBNA) leader protein (EBNALP) is one of the first viral genes expressed upon B-cell infection. EBNALP is essential for EBV-mediated B-cell immortalization. EBNALP is thought to function primarily by coactivating EBNA2-mediated transcription.

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Epstein-Barr virus (EBV) efficiently transforms primary human B cells into immortalized lymphoblastoid cell lines (LCLs), which are extensively used in human genetic, immunological and virological studies. LCLs provide unlimited sources of DNA for genetic investigation, but can be difficult to manipulate, for instance because low retroviral or lentiviral transduction frequencies hinder experiments that require co-expression of multiple components. This unit details Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 engineering for robust LCL genome editing.

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Epstein-Barr virus (EBV) transforms small resting primary B cells into large lymphoblastoid cells which are able to grow and survive in vitro indefinitely. These cells represent a model for oncogenesis. In this unit, variants of conventional clustered regularly interspaced short palindromic repeats (CRISPR), namely the CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) methods, are discussed in the context of gene regulation at genomic DNA promoter and enhancer elements.

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Epstein-Barr virus (EBV) causes endemic Burkitt lymphoma (BL) and immunosuppression-related lymphomas. These B cell malignancies arise by distinct transformation pathways and have divergent viral and host expression programs. To identify host dependency factors resulting from these EBV+, B cell-transformed cell states, we performed parallel genome-wide CRISPR/Cas9 loss-of-function screens in BL and lymphoblastoid cell lines (LCLs).

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